4 - Tertiary Structure and Fibrous Proteins Flashcards
Which amino acids are fluorescent?
Trp and Tyr
What does the extinction coefficient tell you?
How easily a molecule catches photons (absorbance)
Which amino acid has the highest extinction coefficient at 280 nm?
Trp
What does it mean to be fluorescent?
It can release an electron when a photon is absorbed
How come Trp and Tyr are fluorescent?
They are rigid (aromatic rings) to not move around, so they release energy
What technique uses the fluorescence of Trp?
FRET
What is Trp’s fluorescence dependent on?
Its microenvironment
What happens if Trp is in a more hydrophobic environment?
Higher energy –> shorter wavelength
What happens if Trp is in a more hydrophilic environment?
Lower energy -> longer wavelength
What is protein primary structure?
Covalent amino acid sequence
What is protein secondary structure?
Alpha helix and beta sheet stabilized by noncovalent interactions
What is protein tertiary structure?
Folding of local secondary structure to form final folded structure
What is protein quaternary structure?
Association of monomers to oligomers
What is a polymer chemist’s view on a protein?
View as a polymer with nodes that can rotate to give the lowest energy
What is a peptide bond?
The amide bond in the polypeptide chain
What is the configuration of the peptide bond?
Planar
How come the peptide bond is planar?
It has double bond character, so it cannot rotate
How much shorter is a peptide bond compared to a C-N bond?
0.13 A shorter
How many J of resonance energy is in a peptide bond?
85 kJ/mol
Are peptide bonds usually trans or cis?
Trans
Which amino acid can have cis conformation?
Pro
How come Pro can be cis?
It has a ring to tie back the polypeptide, and help lock it into the cis conformation
What is the trans:cis ratio of an amino acid that proceeds Pro?
10:1 - 20:1
Why would a cis bond proceed a Pro?
It can break helices and beta-sheets by disrupting H-bonds and sterics
How can an amino acid go from trans to cis?
Through enzymes
How do isomerases for trans to cis amino acids work?
They form a tetrahedral intermediate to allow for free rotation before locking it back into place
What does peptidyl prolyl cis-trans isomerase do?
Converts trans-Pro into cis-Pro
By how much does peptidyl prolyl cis-trans isomerase lower the activation energy?
By 6-8 kcal/mol
What dictates polypeptide conformation?
Dihedral angles around Ca-N and Ca-C=O bonds
What is the phi angle?
Angle around Ca-N
What is the psi angle?
Angle around Ca-C=O
What does a Ramachandran plot describe?
The steric constraints on phi/psi that limit the conformational range of polypeptide backbone
What is the largest area on the Ramachandran plot?
Beta-sheet
What is the smallest area on the Ramachandran plot?
Alpha helix
What angles lead to a beta-sheet?
phi: -180 to -60, psi: 30 to 180
What angles lead to an alpha helix?
phi: -30 to -180, psi: -30 to -70
Which amino acid has the most conformational freedom?
Gly
What does the Ramachandran plot look like for Gly?
Large availability around the corners
Which amino acid has the least conformational freedom?
Pro
What does the Ramachandran plot look like for Pro?
One small strip
How does a Ramachandran plot explain an alpha helix?
Steric cliash at phi = 180, psi = 0, so rotate phi to releave steric clash
What shape are the majority of alpha helices?
Right handed
What H-bonds are present in an alpha helix?
Backbone of C=O with NH 4 amino acids down
What dipoles are present in an alpha helix?
Along amide bond, aligned to reinforce dipoles (electrostatics)
What are the common configurations for an alpha helix?
Phi = 60, psi = -50, 3.6 amino acids per turn
What are some other types of alpha helixes?
3/10, pi, and left-handed
Which amino acids are preferred in an alpha helix?
Ala, Glu, Leu, Met
Which amino acids are not preferred in an alpha helix?
Pro, Gly, Ser, Val, Ile, Thr
How are the R groups oriented in an alpha helix?
Extended away from the helix center
What is needed for an H-bond?
A lone pair for an acceptor, and an H for a donor
Where are the weak parts of an alpha helix and why?
The ends, because there are unfulfilled H-bonds at the end
How can the ends of an alpha helix be stabilized?
By capping
Which amino acids are common for N-capping?
Ser, Asp, Thr, Asn
What makes Ser, Asp, Thr, and Asn good for N-capping?
They have a lone pair (H-bond acceptor) in the right location for the NH donor
Which amino acids are common for C-capping?
Gly
What makes Gly good for C-capping?
It can adopt a left handed conformation to allow for NH to be a donor for the two helical carbonyls
Where does the dipole originate in an alpha helix?
The amide bond (0.5-0.7 unit charge on N-terminus)
True or false: alpha helices can be ampipathic?
True: they can have distinct faces
How can you tell if an alpha helix is ampipathic?
By drawing a helical wheel diagram
How do you draw a helical wheel diagram?
By drawing each amino acid 100 degrees (a little more than 90, 3.6 amino acids per turn) from the previous one
